LAMMPS (23 Jun 2022) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_KeithFantauzziJacob_2010_AuO__SM_974345878378_001 # For Simulator : LAMMPS 28 Feb 2019 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.1652847 4.1652847 4.1652847 Created orthogonal box = (0 -41.652847 0) to (4.1652847 41.652847 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1652847 4.1652847 4.1652847 Created 40 atoms using lattice units in orthogonal box = (0 -41.652847 0) to (4.1652847 41.652847 4.1652847) create_atoms CPU = 0.000 seconds 40 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1652847 4.1652847 4.1652847 Created 42 atoms using lattice units in orthogonal box = (0 -41.652847 0) to (4.1652847 41.652847 4.1652847) create_atoms CPU = 0.000 seconds 42 atoms in group lower Displacing atoms ... WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:98) Reading potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXvZUYZL/ffield.reax.AuO with DATE: 2011-02-18 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 14 1 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (3) fix qeq/reax, perpetual, copy from (2) attributes: half, newton off pair build: copy stencil: none bin: none Deleted 2 atoms, new total = 80 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/SM_974345878378_001#item-citation - pair reaxff command: - fix qeq/reaxff command: The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 14 1 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 158.9 | 158.9 | 158.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6916.627 0 -6916.627 -0.042714855 1 0 -6916.627 0 -6916.627 -0.042714855 Loop time of 0.0727534 on 1 procs for 1 steps with 80 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6916.62698767134 -6916.62698767134 -6916.62698767132 Force two-norm initial, final = 2.2006825e-06 7.3218337e-07 Force max component initial, final = 1.1001909e-06 3.6585197e-07 Final line search alpha, max atom move = 1 3.6585197e-07 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.070666 | 0.070666 | 0.070666 | 0.0 | 97.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010742 | 0.00010742 | 0.00010742 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.0018923 | 0.0018923 | 0.0018923 | 0.0 | 2.60 Other | | 8.792e-05 | | | 0.12 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4918 ave 4918 max 4918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29620 ave 29620 max 29620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29620 Ave neighs/atom = 370.25 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : real Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 158.9 | 158.9 | 158.9 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -6916.627 0 -6916.627 -0.042714855 1445.3202 2 0 -6916.627 0 -6916.627 -0.00026138432 1445.3202 Loop time of 0.0879111 on 1 procs for 1 steps with 80 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6916.62698767131 -6916.62698767131 -6916.62698767056 Force two-norm initial, final = 0.0015594801 9.6574296e-06 Force max component initial, final = 0.00090173105 6.5635438e-06 Final line search alpha, max atom move = 1 6.5635438e-06 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.085648 | 0.085648 | 0.085648 | 0.0 | 97.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.5142e-05 | 7.5142e-05 | 7.5142e-05 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.0019609 | 0.0019609 | 0.0019609 | 0.0 | 2.23 Other | | 0.0002272 | | | 0.26 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4918 ave 4918 max 4918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29620 ave 29620 max 29620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29620 Ave neighs/atom = 370.25 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 14 1 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard (4) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 159 | 159 | 159 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6916.627 0 -6916.627 -0.00026138396 Loop time of 9.82e-07 on 1 procs for 0 steps with 80 atoms 305.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.82e-07 | | |100.00 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4918 ave 4918 max 4918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29620 ave 29620 max 29620 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29620 Ave neighs/atom = 370.25 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 159 | 159 | 159 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -299.93333 -6916.627 4.1652847 83.305694 4.1652847 -0.00026138439 -0.00026484774 -0.00023951177 -0.00031551958 -0.00023951186 2.9453011 1.2662819e-16 Loop time of 8.21e-07 on 1 procs for 0 steps with 80 atoms 243.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 8.21e-07 | | |100.00 Nlocal: 80 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4918 ave 4918 max 4918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29620 ave 29620 max 29620 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30400 ave 30400 max 30400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30400 Ave neighs/atom = 380 Neighbor list builds = 0 Dangerous builds = 0 80 -299.933331334989 eV 2.945301054196 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00